The Quarry will excavate a 9x9 or an area specified with landmarks. It will continue mining down until it reaches bedrock or lava. There is the option to adjust the size of the quarry using landmarks. The Quarry must be powered by a redstone clock. On starting, the Quarry will start building its frame and clear the area within it. Any blocks it replaces or clears are simply dropped. Once the frame is complete, it will spawn a crane-like structure that will begin to mine the area one block at a time. These blocks will "pop out" from the Quarry, unless a pipe is attached to take the items. There is no need for a wood pipe to fetch the items, the Quarry will place the items into a connected stone, cobblestone, gold pipe,iron pipe or diamond pipe on its own. If the quarry encounters lava while digging, the rest of the blocks under the lava will not be mined. If the lava is turned to obsidian or cobblestone, the quarry will return to mining those blocks again, ensuring the entire area is dug out. If the quarry has finished all it can (all the bottom of the quarry is bedrock or lava) then it will need to be replaced before it will mine again. ( In SSP, if you have removed the lava after it has finished and gets "stuck", you can simply save and rejoin your game, and the quarries will work again. )

The Quarry is instrumental if you would like to create a system that converts blocks into items, and back again, without player intervention. Under this system, blocks that you would like to place into pipes are pushed into the quarry area at a high level, so that the quarry will constantly mine these blocks and place them into Pipes.

If the quarry is close to finishing, or you are in danger of stopping the quarry, place a Builder on top of the Quarry and put sand or gravel in it. The sand will be built and it will fall into the Quarry. The Quarry will mine the sand or gravel, which can be piped, through a filter, back to the Builder. This will ensure that the Quarry will never stop working.

The landmarks can specify an area up to 64x64, giving a maximum possible quarry size of 62x62. An area this large provides a low-maintenance quarry that doesn't need replacing nearly as frequently as the default 9x9 quarry, but be advised that mining from a quarry this large takes more than one hour per layer. Also, a few layers will fill several chests of sand, dirt and cobblestone, depending on the selected region (there is a lot of dirt and sand under water).

By placing the frame above water, or by placing a water source block on the first layer of the quarry, any lava encountered will immediately turn into cobblestone or obsidian, avoiding delays. The water will also prevent hostile mob spawning.

Mining in this fashion requires very little additional interaction from the player and is nearly fully automated, but is considerably less time-efficient than mining manually, and in particular, gathering the ores encrusted in the walls of a cave while exploring it. A good way to take advantage of both cases is to select a relatively small area to dig (the default is good) and to gather any ore visible on the walls of the quarry once it is finished.